Pre-processing of the data

ls_preprocessed <- preprocess_rna(path_rnaseq = 'rnaseq.RData', correct_batch = T, correct_gender = T)

Exploring data

Batch effect correction

print(ls_preprocessed$pbatch_bf)

print(ls_preprocessed$pgender_bf)

print(ls_preprocessed$pbatch_af)

print(ls_preprocessed$pgender_af)

DE analysis

gn <- as.character(ls_preprocessed$rna_all$Feature[which(ls_preprocessed$rna_all$Feature_gene_name =='BAP1')])
DE_res <- DE_analysis(ls_preprocessed, 
           GeneBased=TRUE, 
           pDataBased=FALSE,
           NewCondition=FALSE,
           cond_nm= gn,
           reference = 'low', 
           correct_gender=TRUE,
           extremes_only=TRUE)
## Unlist done
## Labeling done
## Filtering done
## factor levels were dropped which had no samples
## Design done
## factor levels were dropped which had no samples
## Warning: Setting row names on a tibble is deprecated.
## vsd symbols done
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 1192 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## DESeq done
## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
## 
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895
## res symbols done
## list done

DE results

heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)

x <- DE_res$res_df %>%
  arrange(desc(abs(log2FoldChange)))
rownames(x) <- make.names(x$symbol, unique = T)
k <- gn
x <- x[-which(x$gene %in%k),]
#head(x, 10)
vp <- volcano_plot(x, gene=NULL, p_title='BAP1', pCutoff=0.001, FCcutoff=1.5)

List of genes differentially expressed (-1.5 > fold change > 1.5, pval<0.001)

vp_tb <- vp$data[which(vp$data$Sig == 'FC_P'),]
rownames(vp_tb) <- c(1:nrow(vp_tb))
kable(vp_tb)
baseMean log2FoldChange lfcSE stat pvalue padj gene symbol Sig lab xvals yvals
6.395729e+01 3.905607 0.4079837 4.461556 0.0000081 0.0001766 ENSG00000263076.1 RPS9 FC_P RPS9 3.905607 0.0000081
7.434226e+01 -3.602810 0.3643107 -3.743773 0.0001813 0.0019834 ENSG00000094755.12 GABRP FC_P GABRP -3.602810 0.0001813
3.568936e+02 -3.477134 0.4061124 -8.802162 0.0000000 0.0000000 ENSG00000139144.5 PIK3C2G FC_P PIK3C2G -3.477134 0.0000000
1.364547e+02 -3.181504 0.3879255 -6.556765 0.0000000 0.0000000 ENSG00000109511.6 ANXA10 FC_P ANXA10 -3.181504 0.0000000
5.915634e+00 -3.075488 0.4096229 -3.759272 0.0001704 0.0018910 ENSG00000180251.4 SLC9A4 FC_P SLC9A4 -3.075488 0.0001704
1.680560e+02 -2.851171 0.4087265 -7.344544 0.0000000 0.0000000 ENSG00000198758.6 EPS8L3 FC_P EPS8L3 -2.851171 0.0000000
3.089430e+01 -2.779230 0.4053354 -6.896032 0.0000000 0.0000000 ENSG00000139151.10 PLCZ1 FC_P PLCZ1 -2.779230 0.0000000
8.698395e+00 -2.763408 0.4376922 -4.052550 0.0000507 0.0007386 ENSG00000213759.4 UGT2B11 FC_P UGT2B11 -2.763408 0.0000507
1.700950e+01 -2.663663 0.4038956 -3.577265 0.0003472 0.0032632 ENSG00000179674.2 ARL14 FC_P ARL14 -2.663663 0.0003472
1.565666e+01 -2.659716 0.4341733 -6.456752 0.0000000 0.0000000 ENSG00000255960.1 RP11-459D22.1 FC_P RP11.459D22.1 -2.659716 0.0000000
8.598807e+00 -2.537779 0.3983237 -6.222362 0.0000000 0.0000001 ENSG00000206918.1 RNU6-1181P FC_P RNU6.1181P -2.537779 0.0000000
1.703118e+01 -2.437372 0.3881446 -6.224429 0.0000000 0.0000001 ENSG00000264727.1 RP11-680C21.1 FC_P RP11.680C21.1 -2.437372 0.0000000
5.309453e+01 -2.432980 0.3995047 -6.091562 0.0000000 0.0000001 ENSG00000255745.1 RP11-625L16.1 FC_P RP11.625L16.1 -2.432980 0.0000000
4.953813e+01 -2.421761 0.4028772 -6.188719 0.0000000 0.0000001 ENSG00000231738.6 TSPAN19 FC_P TSPAN19 -2.421761 0.0000000
5.463126e+01 -2.361731 0.4178989 -6.202472 0.0000000 0.0000001 ENSG00000180861.5 C12orf36 FC_P C12orf36 -2.361731 0.0000000
1.050103e+01 -2.256090 0.4354248 -5.374849 0.0000001 0.0000042 ENSG00000272609.1 RP11-461M2.2 FC_P RP11.461M2.2 -2.256090 0.0000001
1.777785e+03 -2.246058 0.3260558 -6.891107 0.0000000 0.0000000 ENSG00000106258.9 CYP3A5 FC_P CYP3A5 -2.246058 0.0000000
1.145266e+01 -2.221131 0.4247219 -3.961601 0.0000744 0.0009940 ENSG00000096006.7 CRISP3 FC_P CRISP3 -2.221131 0.0000744
3.845727e+02 2.216497 0.3960091 5.543714 0.0000000 0.0000020 ENSG00000178343.4 SHISA3 FC_P SHISA3 2.216497 0.0000000
4.740936e+01 -2.211727 0.3842247 -5.745174 0.0000000 0.0000008 ENSG00000185860.9 C1orf110 FC_P C1orf110 -2.211727 0.0000000
2.762336e+00 -2.189313 0.4089859 -5.199607 0.0000002 0.0000092 ENSG00000234497.1 RP4-612J11.1 FC_P RP4.612J11.1 -2.189313 0.0000002
9.540603e+00 -2.167287 0.4045146 -5.321060 0.0000001 0.0000054 ENSG00000265374.1 RP11-57J16.1 FC_P RP11.57J16.1 -2.167287 0.0000001
6.927466e+00 -2.161285 0.3843989 -5.528617 0.0000000 0.0000021 ENSG00000224493.1 RP11-87O11.1 FC_P RP11.87O11.1 -2.161285 0.0000000
2.699128e+00 -2.150376 0.3770574 -5.482018 0.0000000 0.0000026 ENSG00000201392.1 RNU6-1078P FC_P RNU6.1078P -2.150376 0.0000000
2.632303e+00 -2.136931 0.3878510 -5.353384 0.0000001 0.0000047 ENSG00000231080.1 RP11-342H21.2 FC_P RP11.342H21.2 -2.136931 0.0000001
1.046986e+02 -2.136067 0.4013775 -5.870197 0.0000000 0.0000004 ENSG00000198643.2 FAM3D FC_P FAM3D -2.136067 0.0000000
8.313274e+01 -2.126918 0.3681818 -5.774856 0.0000000 0.0000007 ENSG00000118492.12 ADGB FC_P ADGB -2.126918 0.0000000
6.619559e+00 -2.122946 0.3769792 -5.495207 0.0000000 0.0000024 ENSG00000254878.1 CTD-3096P4.1 FC_P CTD.3096P4.1 -2.122946 0.0000000
2.223428e+02 -2.121234 0.4131340 -5.221776 0.0000002 0.0000084 ENSG00000166959.3 MS4A8 FC_P MS4A8 -2.121234 0.0000002
9.753472e+00 -2.119295 0.4378337 -5.141038 0.0000003 0.0000118 ENSG00000255892.1 RP11-459D22.2 FC_P RP11.459D22.2 -2.119295 0.0000003
3.292266e+00 -2.117288 0.4184216 -4.734363 0.0000022 0.0000632 ENSG00000253622.1 RP11-654G14.1 FC_P RP11.654G14.1 -2.117288 0.0000022
3.057300e+01 -2.102215 0.3593455 -5.852412 0.0000000 0.0000004 ENSG00000183644.9 C11orf88 FC_P C11orf88 -2.102215 0.0000000
3.057907e+00 -2.099597 0.4040851 -5.079014 0.0000004 0.0000154 ENSG00000221436.1 MIR548F3 FC_P MIR548F3 -2.099597 0.0000004
1.887166e+01 -2.092479 0.3489431 -5.970496 0.0000000 0.0000003 ENSG00000124564.13 SLC17A3 FC_P SLC17A3 -2.092479 0.0000000
3.284765e+01 -2.069994 0.3722642 -5.587361 0.0000000 0.0000016 ENSG00000152936.6 IFLTD1 FC_P IFLTD1 -2.069994 0.0000000
5.937833e+00 -2.062259 0.4092754 -5.138920 0.0000003 0.0000119 ENSG00000269916.1 RP11-193M21.1 FC_P RP11.193M21.1 -2.062259 0.0000003
1.454277e+02 -2.043549 0.3876956 -5.264933 0.0000001 0.0000069 ENSG00000015520.10 NPC1L1 FC_P NPC1L1 -2.043549 0.0000001
3.642398e+02 -2.040786 0.4052670 -5.161997 0.0000002 0.0000108 ENSG00000171747.4 LGALS4 FC_P LGALS4 -2.040786 0.0000002
4.116681e+00 -2.023286 0.4150570 -4.806811 0.0000015 0.0000468 ENSG00000236164.1 RP11-268F1.3 FC_P RP11.268F1.3 -2.023286 0.0000015
3.250756e+01 -2.018262 0.2342670 -4.315903 0.0000159 0.0002980 ENSG00000137860.7 SLC28A2 FC_P SLC28A2 -2.018262 0.0000159
1.147143e+01 -2.015023 0.4319118 -4.890826 0.0000010 0.0000333 ENSG00000176571.7 CNBD1 FC_P CNBD1 -2.015023 0.0000010
3.843674e+02 -2.008995 0.3289891 -6.107607 0.0000000 0.0000001 ENSG00000174844.10 DNAH12 FC_P DNAH12 -2.008995 0.0000000
5.518288e+01 -1.994169 0.3984189 -4.943332 0.0000008 0.0000269 ENSG00000113303.7 BTNL8 FC_P BTNL8 -1.994169 0.0000008
3.534691e+01 -1.972888 0.4013390 -4.933334 0.0000008 0.0000281 ENSG00000224259.1 RP11-48O20.4 FC_P RP11.48O20.4 -1.972888 0.0000008
1.913498e+02 -1.972476 0.3265393 -6.078994 0.0000000 0.0000001 ENSG00000179813.2 FAM216B FC_P FAM216B -1.972476 0.0000000
2.915134e+00 -1.967581 0.4173450 -4.620100 0.0000038 0.0000986 ENSG00000250961.1 CTD-2023N9.1 FC_P CTD.2023N9.1 -1.967581 0.0000038
6.459530e+00 -1.955358 0.4266388 -4.812671 0.0000015 0.0000456 ENSG00000109205.12 ODAM FC_P ODAM -1.955358 0.0000015
1.060466e+02 -1.950554 0.4303060 -4.570237 0.0000049 0.0001187 ENSG00000101076.12 HNF4A FC_P HNF4A -1.950554 0.0000049
4.903937e+01 -1.941008 0.3795627 -4.909471 0.0000009 0.0000310 ENSG00000259871.1 CTA-363E6.1 FC_P CTA.363E6.1 -1.941008 0.0000009
1.654734e+01 -1.927166 0.3398336 -5.655685 0.0000000 0.0000012 ENSG00000152595.12 MEPE FC_P MEPE -1.927166 0.0000000
4.787161e+01 1.922242 0.3860571 5.020664 0.0000005 0.0000194 ENSG00000156959.7 LHFPL4 FC_P LHFPL4 1.922242 0.0000005
1.619878e+01 -1.914762 0.3512283 -5.458547 0.0000000 0.0000029 ENSG00000178125.10 PPP1R42 FC_P PPP1R42 -1.914762 0.0000000
1.402639e+01 -1.914343 0.3519080 -5.434830 0.0000001 0.0000032 ENSG00000111404.2 RERGL FC_P RERGL -1.914343 0.0000001
4.324700e+00 -1.908944 0.4002577 -4.751821 0.0000020 0.0000588 ENSG00000259833.1 RP11-23E19.1 FC_P RP11.23E19.1 -1.908944 0.0000020
1.723749e+03 -1.908686 0.4054201 -4.736682 0.0000022 0.0000625 ENSG00000125999.6 BPIFB1 FC_P BPIFB1 -1.908686 0.0000022
1.394267e+01 -1.901706 0.4356505 -4.593225 0.0000044 0.0001090 ENSG00000257454.1 CTD-2021H9.2 FC_P CTD.2021H9.2 -1.901706 0.0000044
1.399229e+01 -1.898384 0.3520687 -5.372038 0.0000001 0.0000043 ENSG00000231204.1 AC011752.1 FC_P AC011752.1 -1.898384 0.0000001
6.104181e+00 -1.896846 0.3201263 -5.924827 0.0000000 0.0000003 ENSG00000265042.1 AL137800.1 FC_P AL137800.1 -1.896846 0.0000000
6.337819e+00 -1.885726 0.4142377 -4.584775 0.0000045 0.0001125 ENSG00000230739.1 RP11-331H2.4 FC_P RP11.331H2.4 -1.885726 0.0000045
5.324843e+01 -1.874704 0.3643601 -5.180296 0.0000002 0.0000100 ENSG00000231980.1 AC011899.10 FC_P AC011899.10 -1.874704 0.0000002
1.711681e+02 -1.864090 0.3677366 -5.088596 0.0000004 0.0000147 ENSG00000169064.8 ZBBX FC_P ZBBX -1.864090 0.0000004
4.820517e+01 -1.863829 0.4361304 -4.991890 0.0000006 0.0000221 ENSG00000205922.4 ONECUT3 FC_P ONECUT3 -1.863829 0.0000006
1.055252e+03 -1.862965 0.3902522 -4.904527 0.0000009 0.0000315 ENSG00000127324.4 TSPAN8 FC_P TSPAN8 -1.862965 0.0000009
1.017633e+01 -1.853212 0.3935168 -4.807918 0.0000015 0.0000467 ENSG00000236460.1 SNX2P2 FC_P SNX2P2 -1.853212 0.0000015
1.260226e+02 -1.845505 0.3475012 -5.323896 0.0000001 0.0000053 ENSG00000170324.15 FRMPD2 FC_P FRMPD2 -1.845505 0.0000001
1.157815e+01 -1.834585 0.4364329 -4.584523 0.0000046 0.0001126 ENSG00000229005.2 RP5-881L22.4 FC_P RP5.881L22.4 -1.834585 0.0000046
2.377084e+02 -1.828788 0.3705012 -4.817670 0.0000015 0.0000446 ENSG00000254608.1 RP11-56A10.1 FC_P RP11.56A10.1 -1.828788 0.0000015
4.557000e+00 -1.826705 0.4054238 -4.466473 0.0000080 0.0001739 ENSG00000232462.1 RP11-13E1.5 FC_P RP11.13E1.5 -1.826705 0.0000080
2.690914e+01 -1.822595 0.4110993 -4.486034 0.0000073 0.0001611 ENSG00000186329.5 TMEM212 FC_P TMEM212 -1.822595 0.0000073
1.006642e+01 1.815546 0.4017259 4.335830 0.0000145 0.0002796 ENSG00000227656.3 RPL3P2 FC_P RPL3P2 1.815546 0.0000145
1.067424e+02 -1.808680 0.3697544 -5.089734 0.0000004 0.0000147 ENSG00000115616.2 SLC9A2 FC_P SLC9A2 -1.808680 0.0000004
2.800994e+01 -1.805767 0.3778649 -4.796064 0.0000016 0.0000489 ENSG00000152611.7 CAPSL FC_P CAPSL -1.805767 0.0000016
7.954587e+01 -1.804249 0.4028713 -4.263718 0.0000201 0.0003557 ENSG00000144852.12 NR1I2 FC_P NR1I2 -1.804249 0.0000201
3.353307e+01 -1.803266 0.3597823 -5.000164 0.0000006 0.0000212 ENSG00000231606.1 RP11-344F13.1 FC_P RP11.344F13.1 -1.803266 0.0000006
6.697073e+00 -1.803135 0.4347802 -4.650053 0.0000033 0.0000883 ENSG00000170788.9 DYDC1 FC_P DYDC1 -1.803135 0.0000033
3.387660e+02 -1.794276 0.4286749 -4.220637 0.0000244 0.0004161 ENSG00000183778.13 B3GALT5 FC_P B3GALT5 -1.794276 0.0000244
3.627475e+01 -1.792554 0.3756921 -4.752823 0.0000020 0.0000586 ENSG00000197826.7 C4orf22 FC_P C4orf22 -1.792554 0.0000020
2.899941e+01 -1.788535 0.4356225 -4.513469 0.0000064 0.0001457 ENSG00000233377.1 MTND4P20 FC_P MTND4P20 -1.788535 0.0000064
4.812892e+00 -1.787645 0.3699238 -4.844228 0.0000013 0.0000402 ENSG00000272508.1 RP11-96C23.14 FC_P RP11.96C23.14 -1.787645 0.0000013
2.953442e+01 -1.787242 0.4050641 -4.748168 0.0000021 0.0000596 ENSG00000153822.9 KCNJ16 FC_P KCNJ16 -1.787242 0.0000021
2.071817e+02 -1.786619 0.3557032 -5.359911 0.0000001 0.0000046 ENSG00000173597.4 SULT1B1 FC_P SULT1B1 -1.786619 0.0000001
1.214391e+01 -1.777301 0.2873209 -6.154611 0.0000000 0.0000001 ENSG00000212259.1 RNU6-308P FC_P RNU6.308P -1.777301 0.0000000
2.772308e+00 -1.765928 0.4335961 -4.246971 0.0000217 0.0003783 ENSG00000199798.1 SNORD114-5 FC_P SNORD114.5 -1.765928 0.0000217
1.376221e+01 -1.760880 0.3927977 -4.968263 0.0000007 0.0000242 ENSG00000212384.1 SNORD113-2 FC_P SNORD113.2 -1.760880 0.0000007
1.186392e+03 1.758429 0.3258986 5.672778 0.0000000 0.0000011 ENSG00000272060.1 RNA18S5 FC_P RNA18S5 1.758429 0.0000000
7.782392e+00 -1.742614 0.3480489 -4.976612 0.0000006 0.0000233 ENSG00000252145.1 RNU6-1225P FC_P RNU6.1225P -1.742614 0.0000006
5.614511e+00 -1.741985 0.3239441 -5.322892 0.0000001 0.0000053 ENSG00000267316.1 RP11-879F14.3 FC_P RP11.879F14.3 -1.741985 0.0000001
5.588912e+01 -1.736783 0.3761547 -4.626557 0.0000037 0.0000961 ENSG00000176034.8 CHDC2 FC_P CHDC2 -1.736783 0.0000037
3.671876e+01 -1.735247 0.3888346 -4.132938 0.0000358 0.0005608 ENSG00000179008.4 C14orf39 FC_P C14orf39 -1.735247 0.0000358
2.799997e+01 -1.733726 0.4264337 -4.232982 0.0000231 0.0003975 ENSG00000258053.1 CTD-2021H9.3 FC_P CTD.2021H9.3 -1.733726 0.0000231
2.476614e+01 -1.732557 0.3719044 -4.806639 0.0000015 0.0000468 ENSG00000116785.9 CFHR3 FC_P CFHR3 -1.732557 0.0000015
6.709973e+00 -1.730895 0.3949433 -4.469892 0.0000078 0.0001717 ENSG00000231688.1 RPL21P43 FC_P RPL21P43 -1.730895 0.0000078
4.280093e+00 -1.725939 0.4206881 -4.133070 0.0000358 0.0005607 ENSG00000272474.1 SNORD113-5 FC_P SNORD113.5 -1.725939 0.0000358
2.252063e+02 1.725812 0.4345496 3.674346 0.0002385 0.0024535 ENSG00000184937.8 WT1 FC_P WT1 1.725812 0.0002385
8.437506e+01 -1.725060 0.3861698 -4.336275 0.0000145 0.0002793 ENSG00000261210.1 CLEC19A FC_P CLEC19A -1.725060 0.0000145
2.357202e+01 -1.722434 0.3038579 -5.690980 0.0000000 0.0000010 ENSG00000201852.1 RNU6-702P FC_P RNU6.702P -1.722434 0.0000000
9.747567e+01 -1.721685 0.3738661 -4.475010 0.0000076 0.0001686 ENSG00000188477.8 AC003003.5 FC_P AC003003.5 -1.721685 0.0000076
6.351681e+00 -1.720670 0.4069225 -4.285843 0.0000182 0.0003318 ENSG00000213579.3 RP4-595K12.1 FC_P RP4.595K12.1 -1.720670 0.0000182
9.808668e+00 1.718650 0.3632088 4.523860 0.0000061 0.0001405 ENSG00000238531.1 SNORD105B FC_P SNORD105B 1.718650 0.0000061
2.341197e+00 -1.715618 0.4330651 -3.833136 0.0001265 0.0014934 ENSG00000252266.1 Y_RNA FC_P Y_RNA -1.715618 0.0001265
4.709991e+00 -1.711718 0.3470465 -4.896369 0.0000010 0.0000327 ENSG00000207769.1 MIR586 FC_P MIR586 -1.711718 0.0000010
8.961454e+00 -1.705116 0.2895962 -5.930252 0.0000000 0.0000003 ENSG00000199551.1 RNU6-545P FC_P RNU6.545P -1.705116 0.0000000
6.418227e+00 -1.705062 0.4094651 -4.149423 0.0000333 0.0005303 ENSG00000225738.2 NRG3-AS1 FC_P NRG3.AS1 -1.705062 0.0000333
4.311073e+00 -1.702169 0.4272429 -3.993381 0.0000651 0.0008962 ENSG00000253500.1 AF121898.3 FC_P AF121898.3 -1.702169 0.0000651
1.395055e+02 -1.698388 0.3846098 -4.431054 0.0000094 0.0001989 ENSG00000178965.9 C1orf173 FC_P C1orf173 -1.698388 0.0000094
1.857221e+02 -1.697836 0.4355724 -3.737769 0.0001857 0.0020190 ENSG00000006611.11 USH1C FC_P USH1C -1.697836 0.0001857
2.710706e+01 -1.695581 0.3826837 -4.350390 0.0000136 0.0002666 ENSG00000253496.2 RP11-13N12.1 FC_P RP11.13N12.1 -1.695581 0.0000136
2.727041e+01 1.694221 0.4377222 4.317120 0.0000158 0.0002968 ENSG00000229544.6 NKX1-2 FC_P NKX1.2 1.694221 0.0000158
8.485052e+02 1.687851 0.2883636 5.803415 0.0000000 0.0000006 ENSG00000266219.1 AL592188.8 FC_P AL592188.8 1.687851 0.0000000
1.470123e+02 1.687124 0.3085721 5.392887 0.0000001 0.0000039 ENSG00000252139.1 SCARNA18 FC_P SCARNA18 1.687124 0.0000001
9.626820e+00 -1.686557 0.3331058 -5.200573 0.0000002 0.0000091 ENSG00000253576.1 GS1-5L10.1 FC_P GS1.5L10.1 -1.686557 0.0000002
2.313546e+01 -1.685894 0.2733041 -6.253703 0.0000000 0.0000001 ENSG00000258026.1 RP11-543H12.1 FC_P RP11.543H12.1 -1.685894 0.0000000
6.219826e+00 -1.683636 0.4240010 -3.965518 0.0000732 0.0009812 ENSG00000255993.1 PSMC1P9 FC_P PSMC1P9 -1.683636 0.0000732
1.988843e+01 -1.678026 0.2695354 -6.221283 0.0000000 0.0000001 ENSG00000234523.1 NDUFB1P2 FC_P NDUFB1P2 -1.678026 0.0000000
5.995542e+01 -1.672144 0.3507616 -4.784304 0.0000017 0.0000514 ENSG00000170703.11 TTLL6 FC_P TTLL6 -1.672144 0.0000017
2.595302e+01 -1.670899 0.3929936 -4.280856 0.0000186 0.0003374 ENSG00000133115.7 STOML3 FC_P STOML3 -1.670899 0.0000186
9.164636e+00 -1.667301 0.2625477 -6.319647 0.0000000 0.0000000 ENSG00000216205.1 AC036178.1 FC_P AC036178.1 -1.667301 0.0000000
2.574318e+01 -1.663684 0.3530013 -3.392622 0.0006923 0.0055673 ENSG00000122012.9 SV2C FC_P SV2C -1.663684 0.0006923
9.447488e+02 -1.658676 0.3765336 -4.116985 0.0000384 0.0005914 ENSG00000104237.6 RP1 FC_P RP1 -1.658676 0.0000384
7.777534e+00 -1.657092 0.3628047 -4.537816 0.0000057 0.0001341 ENSG00000223015.1 RNU6-1135P FC_P RNU6.1135P -1.657092 0.0000057
1.077423e+02 -1.657082 0.2425042 -6.846682 0.0000000 0.0000000 ENSG00000117501.10 MROH9 FC_P MROH9 -1.657082 0.0000000
2.692793e+01 1.655353 0.3899967 3.785196 0.0001536 0.0017410 ENSG00000210077.1 MT-TV FC_P MT.TV 1.655353 0.0001536
4.702193e+00 1.653824 0.4018464 4.138235 0.0000350 0.0005508 ENSG00000229172.1 AC073065.3 FC_P AC073065.3 1.653824 0.0000350
5.030414e+00 -1.652382 0.3793573 -4.481994 0.0000074 0.0001638 ENSG00000221249.1 AC004980.1 FC_P AC004980.1 -1.652382 0.0000074
2.152592e+01 -1.651480 0.3030535 -5.625535 0.0000000 0.0000013 ENSG00000271730.1 RP11-787I22.3 FC_P RP11.787I22.3 -1.651480 0.0000000
2.921686e+01 1.649626 0.3594210 4.578599 0.0000047 0.0001151 ENSG00000115138.6 POMC FC_P POMC 1.649626 0.0000047
6.892794e+00 -1.647152 0.4081034 -4.084261 0.0000442 0.0006606 ENSG00000256717.1 AP000797.3 FC_P AP000797.3 -1.647152 0.0000442
1.502092e+00 -1.646279 0.4321745 -3.669846 0.0002427 0.0024882 ENSG00000238770.1 snoU13 FC_P snoU13 -1.646279 0.0002427
6.298731e+00 -1.644446 0.3574308 -4.531219 0.0000059 0.0001366 ENSG00000264470.1 MIR4794 FC_P MIR4794 -1.644446 0.0000059
7.878457e+01 -1.643886 0.3513834 -4.947666 0.0000008 0.0000264 ENSG00000200389.1 RNU6-509P FC_P RNU6.509P -1.643886 0.0000008
5.188219e+00 -1.639926 0.4230211 -4.085930 0.0000439 0.0006566 ENSG00000240666.1 MME-AS1 FC_P MME.AS1 -1.639926 0.0000439
8.337960e+01 -1.638588 0.3654787 -4.487690 0.0000072 0.0001602 ENSG00000165164.8 CXorf22 FC_P CXorf22 -1.638588 0.0000072
1.383801e+01 1.633614 0.4025336 3.744339 0.0001809 0.0019801 ENSG00000237222.3 AC090505.6 FC_P AC090505.6 1.633614 0.0001809
8.191233e+01 -1.632666 0.3806674 -4.093422 0.0000425 0.0006403 ENSG00000223561.2 AC003090.1 FC_P AC003090.1 -1.632666 0.0000425
9.166382e+00 -1.630897 0.3795985 -4.275920 0.0000190 0.0003429 ENSG00000080572.8 PIH1D3 FC_P PIH1D3 -1.630897 0.0000190
2.196298e+01 -1.627392 0.3102061 -5.252599 0.0000001 0.0000073 ENSG00000257467.1 RP11-121G22.3 FC_P RP11.121G22.3 -1.627392 0.0000001
5.341559e+00 -1.625179 0.3598192 -4.437266 0.0000091 0.0001938 ENSG00000246016.2 RP11-1C1.7 FC_P RP11.1C1.7 -1.625179 0.0000091
1.228739e+01 -1.624600 0.3252000 -5.023798 0.0000005 0.0000192 ENSG00000239119.1 RNU7-119P FC_P RNU7.119P -1.624600 0.0000005
1.342024e+01 -1.622414 0.2778539 -5.868876 0.0000000 0.0000004 ENSG00000206700.1 RNU6-723P FC_P RNU6.723P -1.622414 0.0000000
9.077770e+00 -1.618259 0.2876106 -5.678807 0.0000000 0.0000011 ENSG00000199790.1 RNU6-836P FC_P RNU6.836P -1.618259 0.0000000
9.915807e+00 -1.617854 0.4114030 -4.034653 0.0000547 0.0007835 ENSG00000255666.1 RP11-867G2.6 FC_P RP11.867G2.6 -1.617854 0.0000547
1.198596e+01 -1.617547 0.3742146 -4.341998 0.0000141 0.0002737 ENSG00000227274.1 AC005358.3 FC_P AC005358.3 -1.617547 0.0000141
3.609974e+00 -1.616071 0.3590620 -4.570040 0.0000049 0.0001187 ENSG00000201984.1 Y_RNA FC_P Y_RNA.1 -1.616071 0.0000049
1.228715e+01 1.614902 0.3584603 4.449898 0.0000086 0.0001845 ENSG00000146090.11 RASGEF1C FC_P RASGEF1C 1.614902 0.0000086
3.500915e+01 -1.613115 0.3701629 -4.358204 0.0000131 0.0002582 ENSG00000148584.10 A1CF FC_P A1CF -1.613115 0.0000131
1.194109e+05 1.612413 0.2696172 5.942833 0.0000000 0.0000003 ENSG00000264462.1 MIR3648 FC_P MIR3648 1.612413 0.0000000
9.589887e+00 -1.610169 0.4021951 -4.015403 0.0000593 0.0008330 ENSG00000188729.2 OSTN FC_P OSTN -1.610169 0.0000593
1.338768e+00 -1.609817 0.4331838 -3.738311 0.0001853 0.0020170 ENSG00000235858.1 RP11-36D19.8 FC_P RP11.36D19.8 -1.609817 0.0001853
1.176743e+03 1.607707 0.2946436 5.461828 0.0000000 0.0000029 ENSG00000160200.13 CBS FC_P CBS 1.607707 0.0000000
2.057098e+01 -1.606989 0.3661343 -4.298652 0.0000172 0.0003159 ENSG00000100012.7 SEC14L3 FC_P SEC14L3 -1.606989 0.0000172
7.418793e+01 -1.606235 0.3631896 -4.555501 0.0000052 0.0001256 ENSG00000153233.8 PTPRR FC_P PTPRR -1.606235 0.0000052
4.971652e+01 -1.604928 0.3807218 -4.235823 0.0000228 0.0003938 ENSG00000124237.5 C20orf85 FC_P C20orf85 -1.604928 0.0000228
1.953535e+00 -1.603849 0.4243566 -3.702951 0.0002131 0.0022508 ENSG00000260951.1 RP5-978I12.1 FC_P RP5.978I12.1 -1.603849 0.0002131
5.609159e+01 -1.601879 0.3614049 -4.530778 0.0000059 0.0001368 ENSG00000162078.7 ZG16B FC_P ZG16B -1.601879 0.0000059
7.926429e+00 -1.599889 0.4159279 -3.897939 0.0000970 0.0012156 ENSG00000012504.9 NR1H4 FC_P NR1H4 -1.599889 0.0000970
1.287067e+02 -1.595846 0.4306239 -4.025676 0.0000568 0.0008053 ENSG00000166670.5 MMP10 FC_P MMP10 -1.595846 0.0000568
3.109340e+00 -1.594509 0.4348478 -4.104739 0.0000405 0.0006167 ENSG00000268566.1 RP11-687D19.1 FC_P RP11.687D19.1 -1.594509 0.0000405
4.556154e+00 -1.593594 0.4252739 -4.007675 0.0000613 0.0008547 ENSG00000200406.1 SNORD114-23 FC_P SNORD114.23 -1.593594 0.0000613
2.058356e+00 -1.585759 0.4259552 -3.720967 0.0001985 0.0021322 ENSG00000261480.1 RP11-578F21.6 FC_P RP11.578F21.6 -1.585759 0.0001985
2.436957e+01 -1.585755 0.3414095 -4.643281 0.0000034 0.0000905 ENSG00000255555.1 AP000857.3 FC_P AP000857.3 -1.585755 0.0000034
1.769750e+01 -1.584630 0.3374153 -4.718208 0.0000024 0.0000676 ENSG00000259590.1 RP11-20G13.3 FC_P RP11.20G13.3 -1.584630 0.0000024
3.037435e+00 -1.583881 0.4358179 -3.799113 0.0001452 0.0016698 ENSG00000118271.5 TTR FC_P TTR -1.583881 0.0001452
8.163824e+01 -1.583481 0.3471961 -4.632491 0.0000036 0.0000940 ENSG00000114204.10 SERPINI2 FC_P SERPINI2 -1.583481 0.0000036
2.325209e+03 1.583043 0.3464355 4.460830 0.0000082 0.0001769 ENSG00000200795.1 RNU4-1 FC_P RNU4.1 1.583043 0.0000082
1.152383e+02 -1.582556 0.3782377 -4.007530 0.0000614 0.0008549 ENSG00000254142.2 RP11-53M11.3 FC_P RP11.53M11.3 -1.582556 0.0000614
1.221791e+02 -1.580080 0.3069198 -5.194759 0.0000002 0.0000094 ENSG00000100557.5 C14orf105 FC_P C14orf105 -1.580080 0.0000002
4.224641e+02 -1.579226 0.3767903 -4.284184 0.0000183 0.0003338 ENSG00000137968.12 SLC44A5 FC_P SLC44A5 -1.579226 0.0000183
5.322447e+00 1.578842 0.2954826 5.289073 0.0000001 0.0000062 ENSG00000237264.4 FTH1P11 FC_P FTH1P11 1.578842 0.0000001
6.950779e+01 -1.578497 0.2519516 -6.424197 0.0000000 0.0000000 ENSG00000262529.1 CTA-276F8.2 FC_P CTA.276F8.2 -1.578497 0.0000000
1.245443e+01 1.577743 0.3912442 4.002924 0.0000626 0.0008688 ENSG00000199990.1 VTRNA1-1 FC_P VTRNA1.1 1.577743 0.0000626
1.174347e+01 -1.576298 0.3774081 -4.147725 0.0000336 0.0005336 ENSG00000242268.2 RP11-368I23.2 FC_P RP11.368I23.2 -1.576298 0.0000336
4.319028e+00 -1.574790 0.3953339 -3.960813 0.0000747 0.0009963 ENSG00000226409.1 RP11-735G4.1 FC_P RP11.735G4.1 -1.574790 0.0000747
5.758443e+00 -1.572808 0.4042124 -3.741475 0.0001829 0.0019958 ENSG00000250458.2 RP11-107E21.1 FC_P RP11.107E21.1 -1.572808 0.0001829
4.351673e+01 1.571434 0.3941555 3.622933 0.0002913 0.0028535 ENSG00000105697.3 HAMP FC_P HAMP 1.571434 0.0002913
5.105132e+02 -1.570643 0.3691072 -4.271152 0.0000194 0.0003471 ENSG00000007174.13 DNAH9 FC_P DNAH9 -1.570643 0.0000194
4.743095e+02 -1.570048 0.3117129 -5.101661 0.0000003 0.0000139 ENSG00000154678.12 PDE1C FC_P PDE1C -1.570048 0.0000003
1.801050e+01 1.567729 0.3692785 4.004470 0.0000622 0.0008638 ENSG00000216866.4 RPS2P55 FC_P RPS2P55 1.567729 0.0000622
4.369468e+00 -1.566920 0.3462177 -4.455278 0.0000084 0.0001810 ENSG00000232524.1 RP11-332K15.1 FC_P RP11.332K15.1 -1.566920 0.0000084
1.880953e+01 -1.564362 0.4153869 -3.829827 0.0001282 0.0015080 ENSG00000157330.5 C1orf158 FC_P C1orf158 -1.564362 0.0001282
3.260924e+00 -1.564137 0.4185901 -3.665228 0.0002471 0.0025225 ENSG00000225437.1 RP1-257A15.1 FC_P RP1.257A15.1 -1.564137 0.0002471
5.889510e+00 -1.563054 0.3876942 -4.328127 0.0000150 0.0002866 ENSG00000234953.2 RP5-837I24.2 FC_P RP5.837I24.2 -1.563054 0.0000150
8.225308e+00 -1.562651 0.4247699 -3.673057 0.0002397 0.0024625 ENSG00000218476.2 RP11-108N13.1 FC_P RP11.108N13.1 -1.562651 0.0002397
1.671937e+01 -1.561706 0.2657241 -5.937160 0.0000000 0.0000003 ENSG00000238386.1 RNU7-48P FC_P RNU7.48P -1.561706 0.0000000
1.212337e+01 -1.561638 0.3452121 -4.532821 0.0000058 0.0001361 ENSG00000216022.1 AC068062.1 FC_P AC068062.1 -1.561638 0.0000058
1.888402e+04 1.560446 0.2773541 5.573725 0.0000000 0.0000017 ENSG00000169710.6 FASN FC_P FASN 1.560446 0.0000000
1.365552e+01 -1.560404 0.3898377 -3.990055 0.0000661 0.0009061 ENSG00000244649.2 CTD-2377D24.6 FC_P CTD.2377D24.6 -1.560404 0.0000661
8.004087e+01 -1.559638 0.3716590 -4.190781 0.0000278 0.0004621 ENSG00000167858.8 TEKT1 FC_P TEKT1 -1.559638 0.0000278
1.895209e+01 1.559634 0.3956493 3.820144 0.0001334 0.0015581 ENSG00000258794.3 RP11-313F23.5 FC_P RP11.313F23.5 1.559634 0.0001334
1.201455e+02 -1.555338 0.3456697 -4.840664 0.0000013 0.0000407 ENSG00000093134.9 VNN3 FC_P VNN3 -1.555338 0.0000013
2.801601e+01 -1.554479 0.3317998 -4.699404 0.0000026 0.0000730 ENSG00000168589.10 DYNLRB2 FC_P DYNLRB2 -1.554479 0.0000026
8.455202e+00 -1.554318 0.4319698 -3.476687 0.0005077 0.0043667 ENSG00000261713.2 SSTR5-AS1 FC_P SSTR5.AS1 -1.554318 0.0005077
1.808876e+01 -1.553342 0.3238830 -4.779411 0.0000018 0.0000523 ENSG00000239084.1 snoU13 FC_P snoU13.1 -1.553342 0.0000018
1.611715e+01 -1.552972 0.3518433 -4.426809 0.0000096 0.0002018 ENSG00000184617.9 ZNF840 FC_P ZNF840 -1.552972 0.0000096
4.352341e+00 -1.551216 0.4255485 -3.692417 0.0002221 0.0023205 ENSG00000200480.1 SNORD114-28 FC_P SNORD114.28 -1.551216 0.0002221
9.153142e+01 1.551193 0.2290808 6.707414 0.0000000 0.0000000 ENSG00000141965.3 FEM1A FC_P FEM1A 1.551193 0.0000000
6.582343e+00 -1.550812 0.4198405 -3.979807 0.0000690 0.0009366 ENSG00000206889.1 RNU6-1200P FC_P RNU6.1200P -1.550812 0.0000690
3.372070e+02 -1.550550 0.3766542 -4.103474 0.0000407 0.0006189 ENSG00000018625.10 ATP1A2 FC_P ATP1A2 -1.550550 0.0000407
1.618156e+01 -1.550077 0.3671963 -4.209330 0.0000256 0.0004327 ENSG00000255160.1 RP11-428C19.5 FC_P RP11.428C19.5 -1.550077 0.0000256
6.257576e+01 -1.548874 0.3557593 -4.323086 0.0000154 0.0002909 ENSG00000188993.3 LRRC66 FC_P LRRC66 -1.548874 0.0000154
4.963583e+01 -1.547897 0.3744388 -4.510814 0.0000065 0.0001471 ENSG00000165078.7 CPA6 FC_P CPA6 -1.547897 0.0000065
4.597827e+00 -1.546696 0.3739296 -4.174998 0.0000298 0.0004876 ENSG00000228842.2 PCDH9-AS2 FC_P PCDH9.AS2 -1.546696 0.0000298
3.402624e+00 -1.545968 0.3609463 -4.219416 0.0000245 0.0004177 ENSG00000251722.1 RNU5E-3P FC_P RNU5E.3P -1.545968 0.0000245
1.592318e+01 -1.544850 0.3712243 -4.156073 0.0000324 0.0005176 ENSG00000255308.1 RP11-428C19.4 FC_P RP11.428C19.4 -1.544850 0.0000324
5.445472e+00 -1.544404 0.3963451 -3.992229 0.0000655 0.0008999 ENSG00000272958.1 CMP21-97G8.2 FC_P CMP21.97G8.2 -1.544404 0.0000655
9.734185e+01 -1.544195 0.4137684 -3.818666 0.0001342 0.0015650 ENSG00000108242.8 CYP2C18 FC_P CYP2C18 -1.544195 0.0001342
1.362036e+01 -1.542546 0.2748294 -5.607466 0.0000000 0.0000014 ENSG00000252294.1 RNU6-589P FC_P RNU6.589P -1.542546 0.0000000
3.069838e+01 -1.542401 0.2779478 -5.648466 0.0000000 0.0000012 ENSG00000207967.1 MIR620 FC_P MIR620 -1.542401 0.0000000
2.283738e+01 -1.538561 0.3643478 -4.249326 0.0000214 0.0003750 ENSG00000230062.4 ANKRD66 FC_P ANKRD66 -1.538561 0.0000214
8.107794e+00 -1.537181 0.3564991 -4.454194 0.0000084 0.0001817 ENSG00000263652.1 MIR548AX FC_P MIR548AX -1.537181 0.0000084
9.732619e+01 -1.537131 0.3473575 -4.390701 0.0000113 0.0002281 ENSG00000227954.2 RP3-323P13.2 FC_P RP3.323P13.2 -1.537131 0.0000113
3.673474e+01 -1.535843 0.2572689 -6.068152 0.0000000 0.0000002 ENSG00000207286.1 Y_RNA FC_P Y_RNA.2 -1.535843 0.0000000
1.056367e+01 1.534598 0.4376792 3.524911 0.0004236 0.0038063 ENSG00000227599.1 RP4-753D4.2 FC_P RP4.753D4.2 1.534598 0.0004236
1.157003e+01 1.534315 0.3457975 4.402396 0.0000107 0.0002191 ENSG00000214784.4 AC010468.1 FC_P AC010468.1 1.534315 0.0000107
1.470905e+03 1.531104 0.4038813 4.146028 0.0000338 0.0005373 ENSG00000105825.7 TFPI2 FC_P TFPI2 1.531104 0.0000338
2.372372e+01 -1.531027 0.3917049 -3.327857 0.0008752 0.0066873 ENSG00000164756.8 SLC30A8 FC_P SLC30A8 -1.531027 0.0008752
1.126816e+01 -1.530888 0.2796606 -5.488856 0.0000000 0.0000025 ENSG00000252686.1 RNU6-1234P FC_P RNU6.1234P -1.530888 0.0000000
2.088821e+01 -1.529041 0.3241820 -4.758227 0.0000020 0.0000574 ENSG00000261496.1 RP13-514E23.1 FC_P RP13.514E23.1 -1.529041 0.0000020
2.019348e+02 -1.528896 0.3570717 -4.258705 0.0000206 0.0003615 ENSG00000197520.6 FAM177B FC_P FAM177B -1.528896 0.0000206
9.193095e+00 -1.528844 0.4189109 -3.552773 0.0003812 0.0035076 ENSG00000210195.2 MT-TT FC_P MT.TT -1.528844 0.0003812
6.062482e+00 -1.526600 0.3388602 -4.489676 0.0000071 0.0001590 ENSG00000200508.1 Y_RNA FC_P Y_RNA.3 -1.526600 0.0000071
9.732164e+01 1.524814 0.4360688 3.339370 0.0008397 0.0064788 ENSG00000183242.7 WT1-AS FC_P WT1.AS 1.524814 0.0008397
2.548883e+00 -1.523768 0.4326909 -3.582397 0.0003405 0.0032126 ENSG00000239184.1 RNA5SP269 FC_P RNA5SP269 -1.523768 0.0003405
1.434056e+01 -1.522882 0.3702719 -4.199357 0.0000268 0.0004485 ENSG00000254959.2 INMT-FAM188B FC_P INMT.FAM188B -1.522882 0.0000268
1.113133e+01 -1.521503 0.3217797 -4.858058 0.0000012 0.0000381 ENSG00000238388.1 snoU13 FC_P snoU13.2 -1.521503 0.0000012
5.203878e+01 -1.518197 0.3754967 -4.148732 0.0000334 0.0005315 ENSG00000229233.1 AC011891.5 FC_P AC011891.5 -1.518197 0.0000334
5.847675e+00 -1.517882 0.3598884 -4.384626 0.0000116 0.0002336 ENSG00000252210.1 Y_RNA FC_P Y_RNA.4 -1.517882 0.0000116
4.965776e+00 1.517821 0.3416592 4.413374 0.0000102 0.0002108 ENSG00000231977.1 RP5-963E22.4 FC_P RP5.963E22.4 1.517821 0.0000102
3.453608e+00 -1.516391 0.4331745 -3.439144 0.0005836 0.0048748 ENSG00000225417.1 RP5-1178H5.2 FC_P RP5.1178H5.2 -1.516391 0.0005836
2.143091e+00 -1.516257 0.4319315 -3.384969 0.0007119 0.0056858 ENSG00000231720.1 RP11-568A7.3 FC_P RP11.568A7.3 -1.516257 0.0007119
7.190674e+01 -1.515836 0.3226988 -4.691450 0.0000027 0.0000749 ENSG00000089101.13 C20orf26 FC_P C20orf26 -1.515836 0.0000027
2.583663e+01 -1.514908 0.2371353 -6.418420 0.0000000 0.0000000 ENSG00000252496.1 RNA5SP33 FC_P RNA5SP33 -1.514908 0.0000000
2.505869e+01 -1.514818 0.3851561 -3.905180 0.0000942 0.0011889 ENSG00000263429.3 LINC00675 FC_P LINC00675 -1.514818 0.0000942
1.118913e+01 -1.514293 0.2994027 -5.009731 0.0000005 0.0000204 ENSG00000167355.3 AC104389.28 FC_P AC104389.28 -1.514293 0.0000005
1.145388e+01 -1.513706 0.3632942 -4.049824 0.0000513 0.0007452 ENSG00000233005.1 AC067959.1 FC_P AC067959.1 -1.513706 0.0000513
1.016584e+02 -1.510691 0.2915612 -5.178667 0.0000002 0.0000100 ENSG00000197168.7 NEK5 FC_P NEK5 -1.510691 0.0000002
4.730575e+00 -1.508917 0.4280495 -3.435003 0.0005925 0.0049294 ENSG00000258765.1 RP11-692C24.2 FC_P RP11.692C24.2 -1.508917 0.0005925
9.642318e+00 -1.508566 0.3672604 -4.086680 0.0000438 0.0006550 ENSG00000242810.1 MRPL42P6 FC_P MRPL42P6 -1.508566 0.0000438
4.530483e+01 -1.508454 0.4064216 -3.763919 0.0001673 0.0018623 ENSG00000162598.9 C1orf87 FC_P C1orf87 -1.508454 0.0001673
5.599512e+00 -1.508323 0.3003748 -4.984584 0.0000006 0.0000226 ENSG00000222578.1 RNA5SP345 FC_P RNA5SP345 -1.508323 0.0000006
1.726251e+00 -1.506713 0.4357671 -3.528516 0.0004179 0.0037723 ENSG00000230258.2 AC002539.1 FC_P AC002539.1 -1.506713 0.0004179
3.347572e+00 -1.505292 0.3660678 -4.070770 0.0000469 0.0006917 ENSG00000242180.2 OR51B5 FC_P OR51B5 -1.505292 0.0000469
3.816121e+00 -1.505219 0.3516150 -4.263974 0.0000201 0.0003557 ENSG00000273389.1 RP13-514E23.2 FC_P RP13.514E23.2 -1.505219 0.0000201
5.342284e+00 -1.504836 0.3511695 -4.359477 0.0000130 0.0002569 ENSG00000207267.1 RNU6-1081P FC_P RNU6.1081P -1.504836 0.0000130
5.959016e+00 -1.504820 0.3902608 -3.812581 0.0001375 0.0015985 ENSG00000258162.1 RP11-315E17.1 FC_P RP11.315E17.1 -1.504820 0.0001375
8.870222e+01 -1.502227 0.3206199 -4.729730 0.0000022 0.0000644 ENSG00000166596.10 WDR16 FC_P WDR16 -1.502227 0.0000022

Pathway enrichment analysis fGSEA

Low BAP1 is the reference. When BAP1 is high, pathways shown below are up- or down- regulated

fgsea_res <- fgsea_analysis(DE_res)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
HALLMARK_MYC_TARGETS_V2 0.0019841 0.0031048 0.7514702 2.985838 0 57 up
HALLMARK_MYC_TARGETS_V1 0.0019120 0.0031048 0.5951325 2.882789 0 189 up
HALLMARK_DNA_REPAIR 0.0018587 0.0031048 0.5669329 2.639105 0 141 up
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY 0.0019920 0.0031048 0.6926141 2.626220 0 46 up
HALLMARK_P53_PATHWAY 0.0018975 0.0031048 0.5354251 2.595026 0 190 up
HALLMARK_G2M_CHECKPOINT 0.0019120 0.0031048 0.5121996 2.478671 0 187 up
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 0.0019569 0.0031048 0.5601328 2.470739 0 103 up
HALLMARK_E2F_TARGETS 0.0019084 0.0031048 0.5029007 2.432800 0 191 up
HALLMARK_UV_RESPONSE_UP 0.0018484 0.0031048 0.5152321 2.422013 0 147 up
HALLMARK_MITOTIC_SPINDLE 0.0018797 0.0031048 0.4951850 2.409677 0 195 up
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0018939 0.0031048 0.4960800 2.384563 0 175 up
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0018797 0.0031048 0.4853719 2.361925 0 195 up
HALLMARK_INTERFERON_ALPHA_RESPONSE 0.0019417 0.0031048 0.5260215 2.295795 0 93 up
HALLMARK_PI3K_AKT_MTOR_SIGNALING 0.0019569 0.0031048 0.5143544 2.268811 0 103 up
HALLMARK_INTERFERON_GAMMA_RESPONSE 0.0018868 0.0031048 0.4644912 2.256368 0 194 up
HALLMARK_MTORC1_SIGNALING 0.0018975 0.0031048 0.4637870 2.247821 0 190 up
HALLMARK_APOPTOSIS 0.0018519 0.0031048 0.4714723 2.227226 0 155 up
HALLMARK_GLYCOLYSIS 0.0019120 0.0031048 0.4162795 2.014886 0 188 up
HALLMARK_APICAL_JUNCTION 0.0019120 0.0031048 0.4133881 2.002429 0 189 up
HALLMARK_ALLOGRAFT_REJECTION 0.0019120 0.0031048 0.4081824 1.975304 0 187 up
HALLMARK_ADIPOGENESIS 0.0019084 0.0031048 0.4086975 1.969521 0 183 up
HALLMARK_WNT_BETA_CATENIN_SIGNALING 0.0020408 0.0031048 0.5188031 1.923844 0 42 up
HALLMARK_INFLAMMATORY_RESPONSE 0.0018868 0.0031048 0.3906481 1.897625 0 193 up
HALLMARK_MYOGENESIS 0.0018975 0.0031048 0.3863939 1.872722 0 190 up
HALLMARK_IL6_JAK_STAT3_SIGNALING 0.0020492 0.0031048 0.4396043 1.859896 0 82 up
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0018868 0.0031048 0.3751503 1.822342 0 193 up
HALLMARK_CHOLESTEROL_HOMEOSTASIS 0.0019724 0.0031048 0.4383596 1.811611 0 69 up
HALLMARK_HEME_METABOLISM 0.0019194 0.0031048 0.3709272 1.782191 0 179 up
HALLMARK_ESTROGEN_RESPONSE_EARLY 0.0019084 0.0031048 0.3670963 1.775841 0 191 up
HALLMARK_HYPOXIA 0.0019048 0.0031048 0.3686240 1.771905 0 180 up
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
chr19p13 0.0018657 0.0059037 0.7507847 4.048989 0 544 up
chr9q34 0.0018553 0.0059037 0.7295889 3.578502 0 210 up
chr17q25 0.0018762 0.0059037 0.6672525 3.260381 0 202 up
chr3p21 0.0018657 0.0059037 0.6541574 3.210588 0 211 up
chr19q13 0.0018149 0.0059037 0.5602329 3.098032 0 769 up
chr16p11 0.0019157 0.0059037 0.6603864 3.012990 0 120 up
chr11q13 0.0018450 0.0059037 0.5918730 3.009112 0 290 up
chr16q24 0.0020040 0.0059037 0.6331231 2.733117 0 92 up
chr1p31 0.0020833 0.0059037 -0.5831812 -2.646177 0 120 down
chr7p22 0.0020325 0.0059037 0.6055466 2.592822 0 85 up
chr4p16 0.0019194 0.0059037 0.5684632 2.582216 0 118 up
chr22q13 0.0018762 0.0059037 0.5237570 2.573764 0 215 up
chr1q22 0.0020790 0.0059037 0.6570445 2.547734 0 53 up
chr17p13 0.0018149 0.0059037 0.5034765 2.512875 0 236 up
chr7q36 0.0019920 0.0059037 0.5704783 2.511936 0 101 up
chr20q11 0.0019724 0.0059037 0.5282767 2.489806 0 159 up
chr17q21 0.0018450 0.0059037 0.4838084 2.440629 0 271 up
chr12q21 0.0019685 0.0059037 -0.5970674 -2.440323 0 66 down
chr20q13 0.0018382 0.0059037 0.4797197 2.416472 0 265 up
chr12p12 0.0019455 0.0059037 -0.5717705 -2.331402 0 65 down
chr7q22 0.0019724 0.0059037 0.4965144 2.329010 0 153 up
chr5q35 0.0019380 0.0059037 0.5031428 2.328435 0 135 up
chr9p13 0.0018939 0.0059037 0.5079495 2.301112 0 113 up
chr5p13 0.0019455 0.0059037 -0.5355983 -2.298951 0 84 down
chr12q24 0.0018587 0.0059037 0.4558662 2.279257 0 250 up
chr1q21 0.0018762 0.0059037 0.4685764 2.275820 0 191 up
chr8q21 0.0019960 0.0059037 -0.5192316 -2.250271 0 90 down
chr8q22 0.0019455 0.0059037 -0.5240361 -2.249322 0 84 down
chr22q11 0.0018868 0.0059037 0.4528396 2.220897 0 214 up
chr16p13 0.0018282 0.0059037 0.4379570 2.213789 0 272 up
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN 0.0019802 0.0079622 0.7426209 3.761729 0 308 up
LU_EZH2_TARGETS_UP 0.0019194 0.0079622 0.6838918 3.395229 0 257 up
SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP 0.0018832 0.0079622 0.6407552 3.372171 0 444 up
RICKMAN_METASTASIS_DN 0.0019305 0.0079622 0.6842922 3.371849 0 246 up
MARTENS_TRETINOIN_RESPONSE_DN 0.0018182 0.0079622 0.6052181 3.357854 0 722 up
MARTENS_BOUND_BY_PML_RARA_FUSION 0.0019493 0.0079622 0.6332474 3.307524 0 418 up
REACTOME_RRNA_PROCESSING 0.0019305 0.0079622 0.6887952 3.285542 0 184 up
DACOSTA_UV_RESPONSE_VIA_ERCC3_UP 0.0019342 0.0079622 0.6484617 3.278440 0 294 up
KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP 0.0018519 0.0079622 0.5935414 3.275786 0 693 up
WELCSH_BRCA1_TARGETS_DN 0.0019608 0.0079622 0.7266808 3.247569 0 127 up
ENK_UV_RESPONSE_KERATINOCYTE_UP 0.0018484 0.0079622 0.6087051 3.238186 0 487 up
KIM_ALL_DISORDERS_DURATION_CORR_DN 0.0019569 0.0079622 0.7124291 3.230082 0 134 up
REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION 0.0020040 0.0079622 0.7715309 3.228295 0 86 up
REACTOME_EUKARYOTIC_TRANSLATION_INITIATION 0.0019531 0.0079622 0.7426040 3.227236 0 112 up
HSIAO_HOUSEKEEPING_GENES 0.0019231 0.0079622 0.6232810 3.213668 0 362 up
SANSOM_APC_TARGETS_REQUIRE_MYC 0.0019960 0.0079622 0.6661419 3.211729 0 209 up
KEGG_RIBOSOME 0.0020121 0.0079622 0.7683390 3.197411 0 81 up
SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC 0.0019608 0.0079622 0.7394982 3.183014 0 101 up
LI_DCP2_BOUND_MRNA 0.0020080 0.0079622 0.7644617 3.165287 0 78 up
REACTOME_INFLUENZA_INFECTION 0.0019646 0.0079622 0.6891440 3.159990 0 145 up
REACTOME_NONSENSE_MEDIATED_DECAY_NMD 0.0019685 0.0079622 0.7298401 3.151569 0 108 up
REACTOME_METABOLISM_OF_RNA 0.0018975 0.0079622 0.5721733 3.120585 0 626 up
REACTOME_TRANSLATION 0.0019194 0.0079622 0.6252563 3.108811 0 262 up
REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY 0.0019646 0.0079622 0.7258810 3.084952 0 94 up
REACTOME_SELENOAMINO_ACID_METABOLISM 0.0019685 0.0079622 0.7129670 3.068063 0 102 up
KASLER_HDAC7_TARGETS_1_UP 0.0019157 0.0079622 0.6493167 3.067242 0 168 up
AMIT_EGF_RESPONSE_480_HELA 0.0019685 0.0079622 0.6600758 3.051282 0 151 up
LOPEZ_MBD_TARGETS 0.0017857 0.0079622 0.5425486 3.048602 0 885 up
CAIRO_HEPATOBLASTOMA_CLASSES_UP 0.0018587 0.0079622 0.5635591 3.046571 0 560 up
SANSOM_APC_MYC_TARGETS 0.0019531 0.0079622 0.6241811 3.035292 0 224 up
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
SUPT20H_TARGET_GENES 0.0018587 0.0067637 0.5587984 3.191683 0 1169 up
CEBPZ_TARGET_GENES 0.0018116 0.0067637 0.5487399 3.162717 0 1304 up
HDGF_TARGET_GENES 0.0018939 0.0067637 0.5645479 3.132154 0 776 up
SETD7_TARGET_GENES 0.0018868 0.0067637 0.5641538 3.130648 0 786 up
MIR4492 0.0018832 0.0067637 0.5958888 3.110372 0 372 up
ZNF436_TARGET_GENES 0.0019157 0.0067637 0.5883892 3.105689 0 429 up
FXR1_TARGET_GENES 0.0018553 0.0067637 0.5482645 3.098145 0 1002 up
NFKBIA_TARGET_GENES 0.0018051 0.0067637 0.5457988 3.095049 0 1011 up
MIR4283 0.0019417 0.0067637 0.6330661 3.051605 0 194 up
MIR6825_5P 0.0019011 0.0067637 0.5845721 3.051434 0 379 up
THAP1_TARGET_GENES 0.0018832 0.0067637 0.5222676 3.041789 0 1667 up
ADNP_TARGET_GENES 0.0018622 0.0067637 0.5587294 3.033462 0 543 up
KLF14_TARGET_GENES 0.0019268 0.0067637 0.6176392 3.030428 0 215 up
MIR4763_3P 0.0019531 0.0067637 0.6142792 3.029706 0 225 up
RBM34_TARGET_GENES 0.0018519 0.0067637 0.5396694 3.015813 0 846 up
MIR4731_5P 0.0019048 0.0067637 0.6012254 2.992164 0 237 up
KAT5_TARGET_GENES 0.0018622 0.0067637 0.5386702 2.990838 0 768 up
MIR1207_5P 0.0018553 0.0067637 0.5815773 2.966539 0 301 up
EPC1_TARGET_GENES 0.0019048 0.0067637 0.5730291 2.952376 0 332 up
KLF13_TARGET_GENES 0.0018692 0.0067637 0.5059913 2.952132 0 1766 up
MIR486_3P 0.0019455 0.0067637 0.6396048 2.950824 0 153 up
MCM2_TARGET_GENES 0.0020202 0.0067637 0.7176487 2.941038 0 76 up
CIITA_TARGET_GENES 0.0018315 0.0067637 0.5172643 2.936420 0 1039 up
MIR4505 0.0019380 0.0067637 0.5921316 2.936374 0 235 up
MIR423_5P 0.0019231 0.0067637 0.6522103 2.934732 0 129 up
CDC73_TARGET_GENES 0.0018762 0.0067637 0.5417707 2.933345 0 538 up
MIR6721_5P 0.0018484 0.0067637 0.5723532 2.925491 0 308 up
ZNF92_TARGET_GENES 0.0018727 0.0067637 0.5109499 2.920817 0 1183 up
JDP2_TARGET_GENES 0.0018484 0.0067637 0.4999463 2.915312 0 1661 up
MIR6883_5P 0.0018975 0.0067637 0.5551820 2.897276 0 380 up
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
MORF_UBE2I 0.0019493 0.0051258 0.7133588 3.527450 0 219 up
MORF_PHB 0.0019120 0.0051258 0.7680946 3.476173 0 113 up
MORF_NME2 0.0019342 0.0051258 0.7289640 3.408664 0 141 up
MORF_NPM1 0.0019608 0.0051258 0.7185991 3.381004 0 149 up
MORF_CSNK2B 0.0018832 0.0051258 0.6701245 3.380885 0 258 up
MORF_ACTG1 0.0019380 0.0051258 0.7308713 3.366872 0 127 up
MORF_AP2M1 0.0019194 0.0051258 0.6851841 3.362316 0 203 up
MORF_ANP32B 0.0020161 0.0051258 0.6985141 3.358730 0 183 up
MORF_AATF 0.0019802 0.0051258 0.6924533 3.357759 0 191 up
MORF_FBL 0.0019194 0.0051258 0.7240208 3.345283 0 129 up
MORF_RAD23A 0.0018622 0.0051258 0.6429129 3.318616 0 304 up
MORF_DDB1 0.0019268 0.0051258 0.6666799 3.308989 0 226 up
MORF_EIF3S2 0.0019417 0.0051258 0.6676889 3.306004 0 220 up
MORF_TPT1 0.0019531 0.0051258 0.7594675 3.305835 0 92 up
MORF_MAP2K2 0.0019531 0.0051258 0.7265419 3.292324 0 117 up
MORF_IKBKG 0.0019493 0.0051258 0.7139560 3.283910 0 126 up
MORF_DAP3 0.0020243 0.0051258 0.6815812 3.274829 0 179 up
MORF_RAN 0.0019157 0.0051258 0.6511978 3.254191 0 239 up
MORF_RPA2 0.0020161 0.0051258 0.6793347 3.253192 0 176 up
GNF2_EIF3S6 0.0019194 0.0051258 0.7163001 3.228532 0 110 up
MORF_BUB3 0.0019194 0.0051258 0.6462123 3.226195 0 243 up
GCM_CSNK2B 0.0019531 0.0051258 0.7497331 3.214405 0 87 up
MODULE_83 0.0018622 0.0051258 0.6244084 3.199685 0 290 up
MORF_HDAC1 0.0019048 0.0051258 0.6413447 3.197034 0 231 up
GCM_TPT1 0.0020202 0.0051258 0.7992662 3.166444 0 59 up
MORF_CTBP1 0.0020000 0.0051258 0.6673619 3.164312 0 159 up
MODULE_257 0.0019724 0.0051258 0.6704206 3.155993 0 150 up
MORF_PPP1CA 0.0020161 0.0051258 0.6665923 3.141889 0 153 up
MORF_G22P1 0.0020243 0.0051258 0.6599471 3.124111 0 158 up
MORF_GNB1 0.0018832 0.0051258 0.6137062 3.123175 0 274 up
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
GO_VIRAL_GENE_EXPRESSION 0.0019685 0.0101779 0.7022003 3.368700 0 185 up
GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_NONSENSE_MEDIATED_DECAY 0.0019802 0.0101779 0.7260161 3.245483 0 114 up
GO_RIBOSOME_BIOGENESIS 0.0020534 0.0101779 0.6381337 3.200949 0 259 up
GO_STRUCTURAL_CONSTITUENT_OF_RIBOSOME 0.0020284 0.0101779 0.6778943 3.163143 0 152 up
GO_TRANSLATIONAL_INITIATION 0.0019920 0.0101779 0.6601471 3.149390 0 179 up
GO_RIBONUCLEOPROTEIN_COMPLEX 0.0019531 0.0101779 0.5721550 3.144505 0 630 up
GO_RIBOSOMAL_SUBUNIT 0.0020040 0.0101779 0.6578464 3.128156 0 172 up
GO_CYTOSOLIC_RIBOSOME 0.0019157 0.0101779 0.7178149 3.109921 0 95 up
GO_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS 0.0019646 0.0101779 0.5908406 3.099263 0 382 up
GO_LARGE_RIBOSOMAL_SUBUNIT 0.0019960 0.0101779 0.7027448 3.096872 0 108 up
GO_CYTOSOLIC_LARGE_RIBOSOMAL_SUBUNIT 0.0020619 0.0101779 0.8017296 3.086059 0 53 up
GO_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE 0.0019493 0.0101779 0.7162438 3.082829 0 94 up
GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS 0.0019920 0.0101779 0.7665020 3.077570 0 62 up
GO_RIBOSOME 0.0019841 0.0101779 0.6254103 3.050640 0 211 up
GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM 0.0019417 0.0101779 0.6894414 3.039172 0 106 up
GO_RRNA_METABOLIC_PROCESS 0.0020000 0.0101779 0.6305050 3.028541 0 195 up
GO_PROTEIN_TARGETING_TO_MEMBRANE 0.0020040 0.0101779 0.6273435 2.987217 0 173 up
GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS 0.0020080 0.0101779 0.6203842 2.964279 0 189 up
GO_INTERSPECIES_INTERACTION_BETWEEN_ORGANISMS 0.0019194 0.0101779 0.5279694 2.959300 0 859 up
GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE 0.0019646 0.0101779 0.5770295 2.956024 0 296 up
GO_NUCLEOLUS 0.0018622 0.0101779 0.5254808 2.944526 0 837 up
GO_PRERIBOSOME 0.0019841 0.0101779 0.7164599 2.937476 0 71 up
GO_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM 0.0019531 0.0101779 0.6456861 2.929843 0 128 up
GO_MRNA_METABOLIC_PROCESS 0.0019231 0.0101779 0.5267203 2.924927 0 763 up
GO_NCRNA_PROCESSING 0.0020121 0.0101779 0.5697821 2.924319 0 325 up
GO_RNA_BINDING 0.0018215 0.0101779 0.5049426 2.917848 0 1578 up
GO_RNA_PROCESSING 0.0018762 0.0101779 0.5186190 2.902894 0 817 up
GO_RIBOSOME_ASSEMBLY 0.0020325 0.0101779 0.7522069 2.899366 0 52 up
GO_RNA_CATABOLIC_PROCESS 0.0020243 0.0101779 0.5520966 2.878377 0 366 up
GO_NCRNA_METABOLIC_PROCESS 0.0020040 0.0101779 0.5451428 2.856717 0 396 up
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
PRC2_EED_UP.V1_DN 0.0019608 0.0057851 0.6632460 3.169888 0 179 up
PDGF_ERK_DN.V1_DN 0.0019608 0.0057851 0.6401067 2.957151 0 141 up
MYC_UP.V1_UP 0.0019920 0.0057851 0.6054549 2.834592 0 157 up
CYCLIN_D1_UP.V1_UP 0.0019881 0.0057851 0.5709890 2.714571 0 173 up
CAMP_UP.V1_UP 0.0019724 0.0057851 0.5519773 2.635868 0 181 up
RB_P130_DN.V1_UP 0.0019569 0.0057851 0.5636551 2.522018 0 114 up
CYCLIN_D1_KE_.V1_UP 0.0019802 0.0057851 0.5280465 2.518532 0 178 up
RAPA_EARLY_UP.V1_DN 0.0019841 0.0057851 0.5303480 2.507278 0 167 up
IL15_UP.V1_UP 0.0020040 0.0057851 0.5262108 2.502848 0 174 up
SRC_UP.V1_UP 0.0019380 0.0057851 0.5332113 2.480464 0 148 up
E2F1_UP.V1_UP 0.0019881 0.0057851 0.5208068 2.475997 0 173 up
ATF2_UP.V1_UP 0.0019881 0.0057851 0.5151452 2.429911 0 165 up
ESC_J1_UP_EARLY.V1_DN 0.0019960 0.0057851 0.5213551 2.422574 0 153 up
RB_DN.V1_UP 0.0019011 0.0057851 0.5254773 2.389480 0 123 up
PIGF_UP.V1_DN 0.0019724 0.0057851 0.5008974 2.380663 0 169 up
RB_P107_DN.V1_UP 0.0019268 0.0057851 0.5214990 2.376944 0 128 up
SIRNA_EIF4GI_UP 0.0019920 0.0057851 0.5477723 2.345644 0 87 up
RPS14_DN.V1_DN 0.0019841 0.0057851 0.4911143 2.335902 0 172 up
IL2_UP.V1_UP 0.0019802 0.0057851 0.4751610 2.255889 0 170 up
CSR_LATE_UP.V1_UP 0.0019763 0.0057851 0.4796270 2.243683 0 156 up
GCNP_SHH_UP_LATE.V1_DN 0.0019841 0.0057851 0.4743939 2.242749 0 167 up
ESC_V6.5_UP_EARLY.V1_UP 0.0019960 0.0057851 0.4804199 2.229788 0 152 up
ESC_V6.5_UP_LATE.V1_DN 0.0019881 0.0057851 0.4684776 2.209783 0 165 up
MEL18_DN.V1_UP 0.0019417 0.0057851 0.4837492 2.201524 0 129 up
ESC_J1_UP_LATE.V1_DN 0.0020040 0.0057851 0.4613903 2.194538 0 174 up
CSR_EARLY_UP.V1_UP 0.0019455 0.0057851 0.4704720 2.165972 0 139 up
BCAT_BILD_ET_AL_UP 0.0019960 0.0057851 0.5827447 2.155810 0 43 up
CRX_NRL_DN.V1_UP 0.0019011 0.0057851 0.4696732 2.135724 0 123 up
AKT_UP_MTOR_DN.V1_UP 0.0020040 0.0057851 0.4472208 2.109560 0 166 up
RAPA_EARLY_UP.V1_UP 0.0019048 0.0057851 0.4518858 2.105253 0 146 up
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP 0.0018939 0.0027001 0.8136341 3.968296 0 187 up
GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP 0.0019084 0.0027001 0.7489666 3.647362 0 181 up
GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN 0.0018553 0.0027001 0.7370112 3.608971 0 183 up
GSE45837_WT_VS_GFI1_KO_PDC_DN 0.0019194 0.0027001 0.7381046 3.594444 0 180 up
GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN 0.0018939 0.0027001 0.7339672 3.579741 0 187 up
GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP 0.0019268 0.0027001 0.7267557 3.484145 0 162 up
GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN 0.0018553 0.0027001 0.7009428 3.432352 0 183 up
GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN 0.0018975 0.0027001 0.7022270 3.429686 0 191 up
GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN 0.0019011 0.0027001 0.6977299 3.403930 0 189 up
GSE38681_WT_VS_LYL1_KO_LYMPHOID_PRIMED_MULTIPOTENT_PROGENITOR_UP 0.0019120 0.0027001 0.6856263 3.336476 0 179 up
GSE42724_NAIVE_VS_B1_BCELL_DN 0.0019231 0.0027001 0.6795766 3.297390 0 178 up
GSE42021_CD24LO_TREG_VS_CD24LO_TCONV_THYMUS_DN 0.0019048 0.0027001 0.6754033 3.295617 0 185 up
GSE22589_HEALTHY_VS_SIV_INFECTED_DC_UP 0.0019120 0.0027001 0.6695782 3.258381 0 179 up
GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_DN 0.0018975 0.0027001 0.6667556 3.256443 0 191 up
GSE9988_LPS_VS_CTRL_TREATED_MONOCYTE_DN 0.0019120 0.0027001 0.6664943 3.251515 0 193 up
GSE3337_CTRL_VS_16H_IFNG_IN_CD8POS_DC_DN 0.0019194 0.0027001 0.6661061 3.243824 0 180 up
GSE6269_FLU_VS_E_COLI_INF_PBMC_UP 0.0019417 0.0027001 0.6823938 3.229015 0 153 up
GSE43863_NAIVE_VS_LY6C_LOW_CXCR5NEG_CD4_EFF_TCELL_D6_LCMV_DN 0.0019380 0.0027001 0.6680005 3.226660 0 173 up
GSE42021_CD24HI_TREG_VS_CD24HI_TCONV_THYMUS_UP 0.0018553 0.0027001 0.6583079 3.223580 0 183 up
GSE37532_VISCERAL_ADIPOSE_TISSUE_VS_LN_DERIVED_PPARG_KO_TREG_CD4_TCELL_DN 0.0019048 0.0027001 0.6917367 3.213316 0 128 up
GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_UP 0.0019194 0.0027001 0.6586656 3.212405 0 194 up
GSE23568_CTRL_VS_ID3_TRANSDUCED_CD8_TCELL_UP 0.0018939 0.0027001 0.6586150 3.212229 0 187 up
GSE22886_TCELL_VS_BCELL_NAIVE_UP 0.0019011 0.0027001 0.6582875 3.211507 0 189 up
GSE360_L_DONOVANI_VS_B_MALAYI_HIGH_DOSE_MAC_DN 0.0018622 0.0027001 0.6515805 3.193919 0 184 up
GSE21546_UNSTIM_VS_ANTI_CD3_STIM_DP_THYMOCYTES_DN 0.0018553 0.0027001 0.6495656 3.180770 0 183 up
GSE21670_UNTREATED_VS_IL6_TREATED_CD4_TCELL_UP 0.0019120 0.0027001 0.6513792 3.169819 0 179 up
GSE360_L_DONOVANI_VS_T_GONDII_MAC_DN 0.0019048 0.0027001 0.6490942 3.164098 0 188 up
GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN 0.0019048 0.0027001 0.6487939 3.163330 0 190 up
GSE24634_TREG_VS_TCONV_POST_DAY3_IL4_CONVERSION_UP 0.0018832 0.0027001 0.6459728 3.160821 0 182 up
GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_DN 0.0019048 0.0027001 0.6477552 3.158266 0 190 up
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='BAP1 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
chr19p13 0.0018416 0.0064626 0.7507847 4.070163 0 544 up
GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP 0.0019493 0.0064626 0.8136341 3.906648 0 187 up
GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN 0.0019011 0.0064626 0.7426209 3.781248 0 308 up
GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP 0.0019417 0.0064626 0.7489666 3.585050 0 181 up
chr9q34 0.0019646 0.0064626 0.7295889 3.541764 0 210 up
GSE45837_WT_VS_GFI1_KO_PDC_DN 0.0019455 0.0064626 0.7381046 3.536428 0 180 up
GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN 0.0019380 0.0064626 0.7370112 3.535072 0 183 up
GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN 0.0019493 0.0064626 0.7339672 3.524129 0 187 up
MORF_UBE2I 0.0019194 0.0064626 0.7133588 3.492641 0 219 up
MORF_PHB 0.0020080 0.0064626 0.7680946 3.447925 0 113 up
GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP 0.0019646 0.0064626 0.7267557 3.435344 0 162 up
SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP 0.0018939 0.0064626 0.6407552 3.421352 0 444 up
MORF_NME2 0.0019380 0.0064626 0.7289640 3.405198 0 141 up
LU_EZH2_TARGETS_UP 0.0019841 0.0064626 0.6838918 3.397405 0 257 up
RICKMAN_METASTASIS_DN 0.0019493 0.0064626 0.6842922 3.394247 0 246 up
GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN 0.0019646 0.0064626 0.7022270 3.375732 0 191 up
GO_VIRAL_GENE_EXPRESSION 0.0019531 0.0064626 0.7022003 3.368209 0 185 up
GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN 0.0019380 0.0064626 0.7009428 3.362070 0 183 up
MORF_NPM1 0.0019763 0.0064626 0.7185991 3.354154 0 149 up
MARTENS_TRETINOIN_RESPONSE_DN 0.0018149 0.0064626 0.6052181 3.353928 0 722 up
MORF_ANP32B 0.0019380 0.0064626 0.6985141 3.350421 0 183 up
GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN 0.0019724 0.0064626 0.6977299 3.348345 0 189 up
MARTENS_BOUND_BY_PML_RARA_FUSION 0.0019342 0.0064626 0.6332474 3.346672 0 418 up
MORF_CSNK2B 0.0019417 0.0064626 0.6701245 3.342085 0 258 up
MORF_ACTG1 0.0020325 0.0064626 0.7308713 3.335667 0 127 up
MORF_AATF 0.0019646 0.0064626 0.6924533 3.328748 0 191 up
REACTOME_EUKARYOTIC_TRANSLATION_INITIATION 0.0020284 0.0064626 0.7426040 3.327944 0 112 up
MORF_AP2M1 0.0019194 0.0064626 0.6851841 3.321971 0 203 up
WELCSH_BRCA1_TARGETS_DN 0.0020325 0.0064626 0.7266808 3.316542 0 127 up
MORF_FBL 0.0020325 0.0064626 0.7240208 3.313485 0 129 up